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One major constraint is the spread of disease within an aquaculture facility. Pathogens can be introduced from natural sources or through the introduction of new individuals to farm stocks. These animals have also been known to escape, spreading disease to wild populations. When animals are confined to a relatively small space, it is common for diseases and parasites to proliferate and spread rapidly. In Irish salmon farms, outbreaks of Amoebic Gill Disease (AGD) have become more and more frequent in recent years (Palmer et al., 1997). AGD is caused by Neoparamoeba perurans, and attacks the gills of farm raised salmonoid fish, eventually drowning them, and has led to mass mortality across the industry (Ruane and Jones, 2013). Most notably its effects have been recorded in Tazmania, Australia, and Washington, USA, however it has also been recorded in Chile, Norway, Scotland and Ireland.


Marine Harvest salmon farm in Northern Ireland (WWW1)

AGD is identified in commercial farms by utilising a ‘gross gill score’ field evaluation methodology which established the presence and severity of the disease in farmed fish stocks. AGD appears in the early stages of growth at sea subsequent to being moved from freshwater hatcheries to open net sea cages, with symptoms presenting as (WWW2 & 3):

  • Mucoid patches
  • Hyper-plastic lesions
  • Flared operculae and gasping
  • Fish may also appear higher in water column

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Once identified, infected fish stocks can be treated with 2-3hr freshwater bath. Access to freshwater resources may therefore be a key consideration in the planning and development of farmed fishing facilities and may be hindered by restrictions that will be discussed in next week’s blog post “Aquaculture: Need for Space”. Hydrogen peroxide has also been effective in treating symptoms and is a common method used in Ireland (Adams et al., 2012).

Additional environmental impacts have been observed due to fish farming facilities in the form of sea lice infestations on trout stocks. Current research conducted by Inland Fisheries Ireland and Argyll Fisheries Trust (Scotland) suggest that trout caught in close proximity to farmed salmon stock have a higher incidence of sea lice than those caught elsewhere. These results were based on an assessment of lice infestation of 20,000 trout over a 25 year period across  94 river and lake systems in both Ireland and Scotland. Increased levels of sea lice lead to:

  1. increased mortality
  2. reduced body condition
  3. changed migratory behavior

Lice infested sea trout (Shephard et al. 2016, 597)

Salmon farming facilities operate in Bantry Bay, Co. Cork, Roancarrig, Bantry Bay, Co. Cork, with an additional site proposed by Marine Harvest for Shot Head (near Trafrask, Adrigole), Bantry Bay, Co Cork. The licence for this development was approved in 2016 however the Aquaculture Licence Appeals Board (ALAB) will be holding an open discussion on the proposed developments in the coming months (date TBC) in West Cork to address any concerns or queries.

Influence of pathogen spread is also seen in the culture of the Pacific oyster in Co. Cork. This species has shown an increase in production (7%) since 2014 (WWW3), but has the potential to crash due to the spread of disease, which has been shown to give rise to mass mortalities across the UK, France, Spain and Ireland (EFSA, 2009). Financial losses due to these mortalities can have profound effects on the dozens of aquaculture employees in Co. Cork alone, not least the value of the product to the Irish economy as a whole.

Seán & Orla-Peach


Adams, M. B., Crosbie, P. B. B., & Nowak, B. F. (2012) Preliminary success using hydrogen peroxide to treat Atlantic salmon, Salmo salar L., affected with experimentally induced amoebic gill disease (AGD). Journal of Fish Diseases, 35: 839–848.

EFSA (2009) Scientific Opinion of the Panel on Contaminants in the Food Chain on a request from the European Commission on Marine Biotoxins in Shellfish – Summary on regulated marine biotoxins. The EFSA Journal of Agricultural and Food Chemistry, 1306, 1-23.

Palmer, R., Carson, J., Ruttledge, M., Drinan, E., & Wagner, T. (1997). Gill disease associated with Paramoeba, in sea reared Atlantic salmon in Ireland. Bulletin of the European Association of Fish Pathologists, 17: 112–114

Ruane, N. M., & Jones, S. R. M. (2013). Amoebic Gill Disease (AGD) of farmed Atlantic salmon (Salmo salar L.). ICES Identification Leaflets for Diseases and Parasites of Fish and Shellfish, (Leaflet No.60), 6pp.

Shephard S., MacIntyre, C. & Gargan, P.(2016) Aquaculture and environmental drivers of salmon lice infestation and body condition in sea trout.Aquaculture Environment Interactions. Vol. 8: 597–610

WWW1 – Marine Harvest

WWW2 – Gill diseases in seawater-farmed salmon have multiple causes and lead to substantial losses.

WWW3 – Amoebic Gill Disease 

WWW4 – Inland Fisheries Ireland